rs1923834

Variant names:

• chr13-27786350-C-T
• rs1923834

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0787 in 152,132 control chromosomes in the GnomAD database, including 521 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.079 (521 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0787 AC: 11966 AN: 152014 Hom.: 521 Cov.: 32

Gnomad AFR AF: 0.0910

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0795

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.0657

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.0673

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0787 AC: 11974 AN: 152132 Hom.: 521 Cov.: 32 AF XY: 0.0784 AC XY: 5836 AN XY: 74392

African (AFR) AF: 0.0910 AC: 3776 AN: 41486

American (AMR) AF: 0.0793 AC: 1213 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0432 AC: 150 AN: 3470

East Asian (EAS) AF: 0.158 AC: 818 AN: 5176

South Asian (SAS) AF: 0.0551 AC: 266 AN: 4824

European-Finnish (FIN) AF: 0.0657 AC: 696 AN: 10586

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0700 AC: 4761 AN: 67970

Other (OTH) AF: 0.0666 AC: 141 AN: 2116

Alfa AF: 0.0724 Hom.: 1699

Bravo AF: 0.0807

Asia WGS AF: 0.0900 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.61
PhyloP100		-0.13

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1923834; hg19: chr13-28360487;